UGENE Forum - Distance matrix view

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Distance matrix view (Read 11383 times)

Dec 15^th, 2010 at 12:54am

muphta Offline
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Hi!
I am using the UGene software since today. The main purpose for me to install the program was the need to generate distance matrix view of my alignment. I know that it is the essential part of alignment construction, but I could not find the program, which could visualize the matrix.
Is it possible to get the distance matrix view with UGene?

Thanks!

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Reply #1 - Dec 15^th, 2010 at 5:30am

Mikhail Fursov Offline
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Do I understand correcly that you need a matrix filled with values that indicates some distance of one sequence in alignment from another?

If yes, we can add this function quite fast and provide you with an alpha version to test.

Please tell us which distance methods are you interested in?

---
UGENE team

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Reply #2 - Dec 15^th, 2010 at 4:18pm

muphta Offline
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That's it. I need the distance matrix view (with values) for the OTU's definition. I've used to use neighbor-joining methods for the multiple sequence alignment.

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Reply #3 - Dec 15^th, 2010 at 10:44pm

Mikhail Fursov Offline
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Ok, we will try to add this feature and provide you with a preview version next week.

---
UGENE team

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Reply #4 - Dec 15^th, 2010 at 11:00pm

muphta Offline
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thank you very much! I look forward to hearing from you

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Reply #5 - Dec 23^rd, 2010 at 5:02pm

Oleg Godovykh Offline
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Hello, we've implemented distance matrix view, it is available from our new snapshots page: http://ugene.unipro.ru/snapshot.html . To view distance matrix call context menu Statistics -> Generate distance matrix.

In appeared dialog you can choose algorithm to calculate distance. In release we plan to add some more algorithms. If you have some useful measure to compare the sequences - feel free to ask us for realization.

Also, if you want, we can generate not distance matrix but result of neighbor-join algorithm as a result (or make it optional).

« Last Edit: Dec 23^rd, 2010 at 7:10pm by Oleg Godovykh »

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Reply #6 - Dec 23^rd, 2010 at 6:48pm

muphta Offline
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Posts: 9

Unfortunately I could not open this link:

404
Not Found
The requested URL /shapshot.html was not found on this server.

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Reply #7 - Dec 23^rd, 2010 at 7:10pm

Oleg Godovykh Offline
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Sorry for misprint. http://ugene.unipro.ru/snapshot.html

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Reply #8 - Dec 27^th, 2010 at 9:00pm

muphta Offline
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Posts: 9

It works perfectly! Now I can define OTUs in several sets of similar sequences. Concerning the sequence compare method, unfortunately I am not a specialist in this field, thus I can't evaluate the method you used for the software: if it's optimal or not.
It would be great also to have phylogenetic tree as an option for the distance matrix view.
Kind regards

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